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- PDB-7lbl: Structure of Human IgG1 Fc -

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Basic information

Entry
Database: PDB / ID: 7lbl
TitleStructure of Human IgG1 Fc
ComponentsIg gamma-1 chain C region
KeywordsSIGNALING PROTEIN / Effector / IgG / Antibody / Fc
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsFields, J.K. / Sundberg, E.J.
CitationJournal: To Be Published
Title: Silent Antibodies: Generation of Hyperglycosylated FCs to Ablate Effector Functions
Authors: Fields, J.K. / Sundberg, E.J.
History
DepositionJan 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6824
Polymers52,4312
Non-polymers3,2512
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint64 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.523, 79.986, 141.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 237 through 245 or (resid 246...
d_2ens_1(chain "B" and (resid 237 through 360 or (resid 361...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLEUA1 - 207
d_21ens_1GLYLEUB1 - 207

NCS oper: (Code: givenMatrix: (-0.959686237414, -0.0642983386562, -0.273620264899), (0.0650239484936, -0.997863011518, 0.00642622495837), (-0.273448737133, -0.0116247103606, 0.961816330839)Vector: - ...NCS oper: (Code: given
Matrix: (-0.959686237414, -0.0642983386562, -0.273620264899), (0.0650239484936, -0.997863011518, 0.00642622495837), (-0.273448737133, -0.0116247103606, 0.961816330839)
Vector: -39.9413685964, -2.09199474873, -4.84476988449)

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 26215.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PYX1
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: CRYSTALS GROWN BY MIXING 1 UL OF FC (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.05M Phosphate PH7, 20% PEG 3350 pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.13→28.84 Å / Num. obs: 32029 / % possible obs: 99.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 48.79 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Net I/σ(I): 2.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
9.04-28.840.0274920.0121
2.13-2.196.30.76525680.326198.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JII

5jii


Resolution: 2.13→28.84 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1580 4.94 %
Rwork0.2138 30398 -
obs0.2151 31978 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.11 Å2
Refinement stepCycle: LAST / Resolution: 2.13→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 220 60 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133578
X-RAY DIFFRACTIONf_angle_d1.30964882
X-RAY DIFFRACTIONf_chiral_restr0.0698600
X-RAY DIFFRACTIONf_plane_restr0.0102598
X-RAY DIFFRACTIONf_dihedral_angle_d8.4649584
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.53644594574 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.20.36791500.30052681X-RAY DIFFRACTION98.37
2.2-2.280.33771330.28392719X-RAY DIFFRACTION98.14
2.28-2.370.33411390.2682725X-RAY DIFFRACTION98.55
2.37-2.480.30041310.26072740X-RAY DIFFRACTION98.83
2.48-2.610.29021320.25592721X-RAY DIFFRACTION98.65
2.61-2.770.28711550.26162750X-RAY DIFFRACTION99.05
2.77-2.980.27381300.25862738X-RAY DIFFRACTION99.14
2.98-3.280.27241390.25182781X-RAY DIFFRACTION99.02
3.28-3.760.25151500.2292780X-RAY DIFFRACTION99.09
3.76-4.730.18281530.17222820X-RAY DIFFRACTION99.33
4.73-28.840.20071680.17172943X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: -23.3800525205 Å / Origin y: -1.75236209222 Å / Origin z: 25.410066418 Å
111213212223313233
T0.411491720703 Å2-0.018113882666 Å20.0225758536578 Å2-0.319207954219 Å2-0.0036207863109 Å2--0.377962737946 Å2
L1.72973753044 °2-0.510649645483 °20.191511672686 °2-0.594904117937 °20.330332445936 °2--0.262603205007 °2
S-0.033819437421 Å °-0.205789637903 Å °0.190142134951 Å °-0.0952990989876 Å °0.0898314194718 Å °-0.0108340276605 Å °-0.0622221370056 Å °0.0215198374723 Å °8.35023573732E-5 Å °
Refinement TLS groupSelection details: all

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